The microbial communities within the gastrointestinal tract are vital to the digestive process, protection against pathogens and the integrity of the immune system, and multiple factors over the lifetime of an individual can influence and alter the composition of these communities. Host and/or environmental factors can shape the contents of the gut microbiota, but the roles of these factors cannot be established based on previous sampling and analyses. In addition to being essential to the life of their hosts, these gut microbial communities often include bacteria and viruses that are detrimental to their host's health and fitness. Furthermore, the gut microbes harbored by one species can serve as the source of disease in associated species, and it is commonly observed that pathogenic agents have closely similar, and sometimes identical, forms that circulate in related species. Two recent developments have now made it possible for us to obtain the information necessary to address questions pertaining to the dynamics, evolution and transmission of the gut microbiota. The first is the application of high-throughput sequencing technologies that allow us to interrogate at unprecedented depths the complex microbial communities present in the gut. The second is our capacity to investigate sets of samples from great-ape hosts that are more comprehensive in scope than those available for any species, including humans. The proposed research has three broad aims. The first is to examine how environmental and host- related factors shape the bacterial diversity within the gut microbiota. To accomplish this, we will examine the distal gut microbial communities of individual chimpanzees from Gombe National Park, many of which have been monitored and sampled for over a decade. The second aim is to investigate the transmission of infectious bacteria within and across species boundaries. This will be achieved by investigating the gut microbial communities sampled from wild apes over broad areas of central Africa where several species co-occur. Finally, we determine how apes can serve as a primary reservoir of bacteria and viruses in humans by establishing the links between the infectious agents circulating in great apes to those implicated in human disease. PUBLIC HEALTH RELEVANCE: The proposed research investigates the on-going dynamics of gut microbial communities, which are essential to human health by providing protection against pathogens and by stimulating the immune system. Additionally, in-depth knowledge of the microbial communities harbored by non-human primates and their relationship to the human microbiota is critical to health issues because these non- human hosts are known to serve as a primary source for emerging diseases in humans.